Using the rockyIntertidal R package

Getting started

Installation

Step 1. Install R, RStudio, and RTools44 in Software Center

Step 2. Install devtools package in R: 

install.packages('devtools')

Step 3. Install rockyIntertidal from GitHub

Note that whenever the rockyIntertidal package is updated, you can rerun this code to install the latest version.

library(devtools)
install_github("KateMMiller/rockyIntertidal")

Step 4. Load rockyIntertidal R package 

library(rockyIntertidal)

Step 5. Import rocky monitoring data

Note that R is not able to connect to files on Sharepoint or MS Teams (b/c Teams also stores all files on Sharepoint). That means you need to store data package files on your local machine or on a server (e.g. NETN Z drive). Currently, the importData() function only imports queries from the rocky intertidal backend database. Once the data package is completed, the import function will be updated to be able to import csvs, either as individual files or as a zipped file. The latest backend (as far as I know) is on the MS Team here: NPS ACAD Intertidal Zone > Data_Pipeline > Files > NETN_RockyIntertidal_Database_be_20231011.mdb. Note that this is the link to the folder, not the actual database. You’ll need to download the database (or move it to the Z drive).

The default option for importing data adds the data package views (i.e., flatfiles) to an environment called ROCKY to your Environment work space (i.e. Environment tab in top right panel). If you would rather import each individual view into your R session, specify with the new_env argument (e.g., importData(new_env = F)).

Option 1. Import data via data package database file on your computer 

importData(type = 'file',
           path = "C:/NETN/R_Dev/data/rocky/NETN_RockyIntertidal_Database_be_20231011.mdb")

Option 2. Import data via data package database DSN (Data Source Name) on your computer. Note that this is the default setting. As long as you have a named DSN called “rocky_BE” that links to the latest rocky backend database, the code below will run. See Setting up DSN tab for how to set up DSN. 

importData() # easiest
importData(type = 'DSN', odbc = "rocky_BE") # equivalent to line above

Step 5b.Import water temperature data

The water temperature data is stored as separate csvs and so has a different import function and process. The temp logger files will go into your ROCKY environment named the 6 letter location code. The buoy = T loads the buoy data for each park to the ROCKY environment. The simplify = T simplifies the datasets to include only 1 logger measurement per high tide event (for water temp) and 1 buoy record per day. All plotting functions require the simplified data. The latest compiled files are on the Z drive here: “Z:/PROJECTS/MONITORING/Rocky_Intertidal/NETN/5_Data/Data_Files/Temperature/Compiled_HT_water_temps_2011-2022/”. This reminds me that I need to update the data to include 2023.

path = "Z:/PROJECTS/MONITORING/Rocky_Intertidal/NETN/5_Data/Data_Files/Temperature/Compiled_HT_water_temps_2011-2022/"
importWaterTemp(path = path, buoy = T, simplify = T)

Step 6. Play with the data

The functions in the rockyIntertidal package are designed to work with the views, and are the best way to interact with the data to query by park, site, site type, year, parameter, etc. However, if you want to view the raw data, and you imported the data into the ROCKY environment, you can access them with the code below:

# See list of the views
names(ROCKY)

# View one of the views
View(ROCKY$Bolts)

# Assign a view to a data frame named bolts in R. Interact with bolts the way you would work with any normal data frame in R. 
bolts <- ROCKY$Bolts

While this works, the better approach is to use the “getter” functions within the R package, which access the same files, but allow you to also query data based on park, location, years, plot name, species, etc. See the specific getter function tabs for details.

If you want to use the print_head() function that shows output in the markdown, run the code below. This makes the results print cleaner in the markdown report. For your purposes, you can just run: head(dataframe).

print_head <- function(df){
  knitr::kable(df[1:6,]) |> #, table.attr = "style='width:60%;'") |> 
    kableExtra::kable_classic(full_width = F, font_size = 12, 
                              bootstrap_options = c("condensed"))
}

Troubleshooting Built Tools:

If you’re contributing to the package, you’ll need to use build tools to build and install the package to test changes before posting to GitHub. Unfortunately Software Center installs RTools44 in C:/Program Files/, not C:/, which is where RStudio looks for it by default. The following code helps RStudio find RTools. You may occasionally have to rerun this code (except for the usethis line), so keep it handy. You know when you have to rerun the code when you try to rebuild a package, and a window pops up to ask if you want to install missing build files.

# Set r environ to find rtools on opening
usethis::edit_r_environ()
Sys.setenv(PATH = paste("C:\\PROGRA~1\\Rtools44\\bin", Sys.getenv("PATH"), sep=";"))
Sys.setenv(BINPREF = "C:\\PROGRA~1\\Rtools44\\mingw_$(WIN)\\bin\\")

Getting help

Getting (and improving) help

The functions in rockyIntertidal have help documentation like any R package. To view the help, you can go to the Packages tab and click on rockyIntertidal (see below). That will show you all the functions in the package. Clicking on individual functions will take you to the help documentation for that function.

You can also see the help of a function by running, for example: 

?importData

If rockyIntertidal isn’t loaded yet, you’d run: 

?rockyIntertidal::importData

Each function’s help includes a Description, Usage (i.e. function arguments and their defaults), Argument options/definitions, and several examples showing how the function can be used.

This is where you come in! If you notice typos or can think of better descriptions, examples, error messages, etc., please send them my way! After we’re more comfortable with R packages and get versed on GitHub, you’ll be able to make those changes directly in the package. For now, you can just send me your suggestions and I’ll make the changes.

Finally, if you ever want to peak under the hood at the function, you can view it several ways.
  1. Keep F2 key pressed and click on the function name in R. This trick works for many but not all functions in R.

  2. View code in the GitHub katemmiller/rockyIntertidal repo. The functions are in the R folder.

Setting up DSN

Setting up a DSN

  1. Go to Windows Start Menu and search ODBC. Click on ODBC Data Sources (64-bit)
  2. Click on Add, then select Microsoft Access Driver (*.mdb, *.accdb) then click Finish in next menu.

  3. Enter rocky_BE into the Data Source Name (red arrow), click on Select (red circle). In new window, click on C:/ (orange arrow) and find the path to your database. If it’s on the Z drive, then click on the Drives window and select correct Drive. Click on the data package database (yellow arrow). When complete, click OK. Finally, add the name of the database file to the Description (blue arrow), so it’s easier to check whether you’re using the latest version.

  4. If updating an existing DSN, follow similar process, except click on the DSN in the first window and select Configure instead of Add.

get Data functions

Bolt data 

print_head(getBolts(location = "CALISL", plotType = "Photoplot"))
Bolt_ID Plot_ID Site_Name Site_Code State_Code Loc_Name Loc_Code Plot_Name Plot_Type Target_Species Label Bolt_UTM_E Bolt_UTM_N Bolt_UTM_Datum Bolt_UTM_Zone Bolt_NAVD88_Elev Bolt_MLLW_Elev ListOrder Notes
77534CF3-B379-4EDA-ABF3-65335904971B BA9B0150-724F-4CF1-83FA-B0EFB0D51D6F Boston Harbor NRA BOHA MA Calf Island CALISL A1 Photoplot Ascophyllum A1 label 343919.7 343919.7 NAD83 19N 0.095710 1.773710 1.0 NA
B30A77DB-3F52-4EAA-ADFE-C928E40022BC BA9B0150-724F-4CF1-83FA-B0EFB0D51D6F Boston Harbor NRA BOHA MA Calf Island CALISL A1 Photoplot Ascophyllum A1 bolt 01 343919.7 343919.7 NAD83 19N 0.107605 1.785605 1.1 NA
76E44039-730E-445F-8CA0-5CA2A165AD31 BA9B0150-724F-4CF1-83FA-B0EFB0D51D6F Boston Harbor NRA BOHA MA Calf Island CALISL A1 Photoplot Ascophyllum A1 bolt 02 343920.2 4689533.2 NAD83 19N -0.063546 1.614454 1.2 NA
806E1DBE-3E60-4BF0-BB05-FDC1E12BF77E BA9B0150-724F-4CF1-83FA-B0EFB0D51D6F Boston Harbor NRA BOHA MA Calf Island CALISL A1 Photoplot Ascophyllum A1 bolt 03 343920.3 4689533.9 NAD83 19N -0.140115 1.537885 1.3 NA
207948E2-944D-47C2-8E73-33FD82FEB2E3 BA9B0150-724F-4CF1-83FA-B0EFB0D51D6F Boston Harbor NRA BOHA MA Calf Island CALISL A1 Photoplot Ascophyllum A1 bolt 04 343919.9 343919.9 NAD83 19N -0.107108 1.570892 1.4 NA
03DA4ECC-E9B1-4FB4-ACF2-8BBD5EA00E35 068910BC-CD38-4A30-9C39-31456231CBA9 Boston Harbor NRA BOHA MA Calf Island CALISL A2 Photoplot Ascophyllum A2 label 343918.1 343918.1 NAD83 19N 0.257231 1.935231 2.0 NA

Point Intercept Data

These are the transect point intercept distances before elevation is determined. Elevation is calculated in sumPISpecies()

print_head(getPIBoltDistance()) # PointIntercept_BoltDist_C
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Plot_Name Label Elevation_MLLW_m Distance_m Notes_Event
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 01 3.487006 0.00 Sampled on 6/20/13
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 02 3.184000 1.04 Sampled on 6/20/13
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 03 NA 1.53 Sampled on 6/20/13
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 04 2.668736 3.16 Sampled on 6/20/13
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 05 2.543000 3.89 Sampled on 6/20/13
Acadia NP ACAD Schoodic Point SCHPOI 2013-06-19 2013 FALSE T1 T1 bolt 06 2.958020 4.95 Sampled on 6/20/13 
print_head(getPISpecies(location = c("BASHAR", "OTTPOI"))) # PointIntercept_SppDetections
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Plot_Name PI_Distance Spp_Code Spp_Name Event_ID Plot_ID
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 0.0 ROCK Rock 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 0.3 ROCK Rock 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 0.6 WATER Water 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 0.9 ROCK Rock 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 1.2 ROCK Rock 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE T1 1.5 ROCK Rock 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 1C404B99-06C5-4963-8271-9ED1721A57E9

PhotoPlot Cover 

print_head(getPhotoCover(location = c("BASHAR", "OTTPOI"), target_species = "Barnacle"))
Site_Code Loc_Code Plot_Name Target_Species Bolt_UTM_E Bolt_UTM_N Bolt_MLLW_Elev Site_Name Loc_Name Start_Date Year Date_Scored QAQC Spp_Code Spp_Name Category Perc_Cover Notes Scorer Event_ID Plot_ID
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE OTHINV Other Invertebrate Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE CHOMAS Irish Moss (Chondrus / Mastocarpus) Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE CRUCOR Crustose coraline Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE OTHPLA Other Plant Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE ALGBRO Other Algae - Brown Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14
ACAD BASHAR B1 Barnacle 554140.1 554140.1 2.365207 Acadia NP Bass Harbor 2013-06-21 2013 2013-09-03 FALSE ALGGRE Other Algae - Green Species Group 0 NA {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 B0B857F3-2B60-42E5-A24D-27173424DB14

Motile Invert Counts 

print_head(getMotileInvertCounts(park = "ACAD", years = 2013:2021, species = c("LITLIT", "LITOBT", "LITSAX")))
Site_Name Site_Code State_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Plot_Name Spp_Name Spp_Code Damage No.Damage Subsampled Event_ID Plot_ID Bolt_UTM_E Bolt_UTM_N Bolt_MLLW_Elev
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum A1 Common periwinkle (Littorina littorea) LITLIT 0 3 No 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 0 6 No 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum A1 Rough periwinkle (Littorina saxatilis) LITSAX 0 0 No 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Ascophyllum A1 Common periwinkle (Littorina littorea) LITLIT 0 2 No 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 0 1 No 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Ascophyllum A1 Rough periwinkle (Littorina saxatilis) LITSAX 0 0 No 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F 67F474C4-53AA-42A5-AE1C-29D22B47D021 554093.7 4897051 2.786703

Motile Invert Meas 

print_head(getMotileInvertMeas(location = "SHIHAR", years = 2013:2019))
Site_Name Site_Code State_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Plot_Name Spp_Name Spp_Code Measurement Event_ID Plot_ID
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 7 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 8 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 10 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 10 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Common periwinkle (Littorina littorea) LITLIT 10 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum A1 Smooth periwinkle (Littorina obtusata) LITOBT 10 9A29BB59-23EB-47F2-AA34-38DEEFF6409C 58ED9BC5-B195-4C87-A164-3A60C2A1913F

Echinoderm Counts 

print_head(getEchinoCounts(park = "ACAD", years = 2013:2021, species = "STRDRO"))
Site_Name Site_Code State_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Plot_Name Event_ID Plot_ID Spp_Code Count Spp_Name
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Echinoderms X1 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 8BABA85C-BDE8-46DB-9547-51FD78420F9B STRDRO 0 Strongylocentrotus droebachiensis (sea urchin)
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Echinoderms X2 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 E5103CAF-94F8-4AA8-939C-4DFA1AA86255 STRDRO 0 Strongylocentrotus droebachiensis (sea urchin)
Acadia NP ACAD ME Bass Harbor BASHAR 2013-06-21 2013 FALSE Echinoderms X3 3F21A576-2949-4C40-A1F6-C22EE46A8DD7 A73241A6-57E8-483B-A78B-5DEC8DC4D51B STRDRO 0 Strongylocentrotus droebachiensis (sea urchin)
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Echinoderms X1 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F 8BABA85C-BDE8-46DB-9547-51FD78420F9B STRDRO 0 Strongylocentrotus droebachiensis (sea urchin)
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Echinoderms X2 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F E5103CAF-94F8-4AA8-939C-4DFA1AA86255 STRDRO 12 Strongylocentrotus droebachiensis (sea urchin)
Acadia NP ACAD ME Bass Harbor BASHAR 2014-06-21 2014 FALSE Echinoderms X3 24C1A879-5BF9-42AB-9FD1-DC86EA201C6F A73241A6-57E8-483B-A78B-5DEC8DC4D51B STRDRO 0 Strongylocentrotus droebachiensis (sea urchin)

Echinoderm Meas 

print_head(getEchinoMeas(location = "SHIHAR", years = 2013:2019))
Site_Name Site_Code State_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Plot_Name Spp_Name Spp_Code Measurement Event_ID Plot_ID
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 25 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 55 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 56 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 57 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 58 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD
Acadia NP ACAD ME Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms X3 Sea urchin (S. droebachiensis) STRDRO 64 9A29BB59-23EB-47F2-AA34-38DEEFF6409C F05658BD-244E-44A4-ADDA-3187937046BD

Summarize Data

For every get function, there’s a sum function that summarizes the data. This is typically at the location level for a given species and year. For example, averaging across the 3 point intercept transects, or averaging percent cover across the 5 barnacle photoplots. Summary functions are demonstrated below.

Point Intercept Data

This the function where elevation is calculated for point intercept distances along the transects.

print_head(sumPISpecies(location = c("BASHAR", "OTTPOI"))) 
## Warning in sumPISpecies(location = c("BASHAR", "OTTPOI")): There were 5 bolt distance/elevation combinations are impossible and cannot calculate slope between bolts. Either the tape didn't follow ground contour between this and the following bolt or a recording error occured. Slope was converted to 0 for these values. Bolt errors are provided in bolt_checks data.frame in your global environment.
Site_Code Loc_Code Loc_Name Start_Date QAQC Year Plot_Name Label Spp_Name Spp_Code Elevation_MLLW_m elev_first elev_last elev_change Distance_m PI_Distance PI_Elevation
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Rock ROCK 4.51103 4.51103 4.317431 0.1935992 0 0.0 4.511030
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Rock ROCK 4.51103 4.51103 4.317431 0.1935992 0 0.3 4.486524
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Water WATER 4.51103 4.51103 4.317431 0.1935992 0 0.6 4.462018
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Rock ROCK 4.51103 4.51103 4.317431 0.1935992 0 0.9 4.437512
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Rock ROCK 4.51103 4.51103 4.317431 0.1935992 0 1.2 4.413005
ACAD BASHAR Bass Harbor 2013-06-21 FALSE 2013 T1 T1 bolt 01 Rock ROCK 4.51103 4.51103 4.317431 0.1935992 0 1.5 4.388499

PhotoPlot Cover 

print_head(sumPhotoCover(location = c("BASHAR", "OTTPOI"), target_species = c("Ascophyllum", "Barnacle")))
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Spp_Code Spp_Name Category avg_cover median_cover min_cover max_cover q25_cover q75_cover
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ALGBRO Other Algae - Brown Species Group 0.0 0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ALGGRE Other Algae - Green Species Group 0.0 0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ALGRED Other Algae - Red Species Group 0.0 0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ARTCOR Articulated Corallines Species Group 0.0 0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ASCEPI Ascophyllum epibiont Species Group 17.6 22 2 27 14 23
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE Ascophyllum ASCNOD Knotted Wrack (A. nodosum) Species 65.0 63 53 85 56 68

Motile Invert Counts 

print_head(sumMotileInvertCounts(park = "ACAD", years = 2013:2021, species = c("CARMAE", "HEMISAN")))
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Spp_Code Spp_Name count_total count_med count_avg count_min count_max count_l25 count_u75 damaged_total damaged_med damaged_avg damaged_min damaged_max damaged_l25 damaged_u75 notdamaged_total notdamaged_med notdamaged_avg notdamaged_min notdamaged_max notdamaged_l25 notdamaged_u75
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Ascophyllum CARMAE Green crab (Carcinus maenas) 6 0 1.2 0 4 0 2 0 0 0 0 0 0 0 6 0 1.2 0 4 0 2
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Ascophyllum HEMISAN Asian shore crab (H. sanguineus) 0 0 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Barnacle CARMAE Green crab (Carcinus maenas) 0 0 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Barnacle HEMISAN Asian shore crab (H. sanguineus) 0 0 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Fucus CARMAE Green crab (Carcinus maenas) 1 0 0.2 0 1 0 0 0 0 0 0 0 0 0 1 0 0.2 0 1 0 0
Acadia NP ACAD Bass Harbor BASHAR 2019-06-11 2019 FALSE Fucus HEMISAN Asian shore crab (H. sanguineus) 0 0 0.0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.0 0 0 0 0

Motile Invert Meas

Measurements are summarized into 5mm bins.

print_head(sumMotileInvertMeas(location = "SHIHAR", years = 2013:2019))
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Spp_Code Spp_Name Meas_5mm_fac num_meas
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum LITLIT Common periwinkle (Littorina littorea) 10 to 14.9 1
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum LITOBT Smooth periwinkle (Littorina obtusata) 5 to 9.9 13
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum LITOBT Smooth periwinkle (Littorina obtusata) 10 to 14.9 28
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum NUCLAP Dogwhelk (Nucella lapillus) 15 to 19.9 1
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum NUCLAP Dogwhelk (Nucella lapillus) 20 to 24.9 11
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Ascophyllum NUCLAP Dogwhelk (Nucella lapillus) 25 to 29.9 14

Echinoderm Counts 

print_head(sumEchinoCounts(park = "ACAD", years = 2013:2021, species = "STRDRO"))
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Spp_Code Spp_Name count_total count_med count_avg count_min count_max count_l25 count_u75
Acadia NP ACAD Bass Harbor BASHAR 2013-06-21 2013 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 0 0 0.0000000 0 0 0 0.0
Acadia NP ACAD Bass Harbor BASHAR 2014-06-21 2014 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 12 0 4.0000000 0 12 0 6.0
Acadia NP ACAD Bass Harbor BASHAR 2015-06-12 2015 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 5 0 1.6666667 0 5 0 2.5
Acadia NP ACAD Bass Harbor BASHAR 2016-06-28 2016 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 2 0 0.6666667 0 2 0 1.0
Acadia NP ACAD Bass Harbor BASHAR 2017-06-25 2017 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 15 0 5.0000000 0 15 0 7.5
Acadia NP ACAD Bass Harbor BASHAR 2018-05-18 2018 FALSE STRDRO Strongylocentrotus droebachiensis (sea urchin) 18 0 6.0000000 0 18 0 9.0

Echinoderm Meas

Measurements are summarized into 5mm bins.

print_head(sumEchinoMeas(location = "SHIHAR", years = 2013:2019))
## Warning
## in
## any(echo$Measurement):
## coercing
## argument
## of type
## 'double'
## to
## logical
Site_Name Site_Code Loc_Name Loc_Code Start_Date Year QAQC Target_Species Spp_Code Spp_Name Meas_5mm_fac num_meas
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms STRDRO Sea urchin (S. droebachiensis) 25 to 29.9 1
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms STRDRO Sea urchin (S. droebachiensis) 55 to 59.9 4
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms STRDRO Sea urchin (S. droebachiensis) 60 to 64.9 1
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms STRDRO Sea urchin (S. droebachiensis) 65 to 69.9 2
Acadia NP ACAD Ship Harbor SHIHAR 2013-06-22 2013 FALSE Echinoderms STRDRO Sea urchin (S. droebachiensis) 75 to 79.9 2
Acadia NP ACAD Ship Harbor SHIHAR 2014-06-20 2014 FALSE Echinoderms ASTRUB Asterias rubens 5 to 9.9 1

Plot Data

For most getter and summary functions, there are plotting functions with the same suffix. Examples are below.

Species Contours

These plots combine the point intercept data (dots and symbols on the graph) and the photoplot cover data (pie charts) to compare changes across years.

plotSpeciesContours(location = "BASHAR", years = 2013:2018)

## TableGrob (1 x 2) "arrange": 2 grobs
##   z
## 1 1
## 2 2
##       cells
## 1 (1-1,1-1)
## 2 (1-1,2-2)
##      name
## 1 arrange
## 2 arrange
##             grob
## 1 gtable[layout]
## 2 gtable[layout]

Point Intercept Transect

Plot the transect contours faceted on transect number

plotPITransects(location = "SHIHAR", years = 2013:2019)

Point Intercept Species

Plot point intercept species detections summarized as median and middle 50% distribution of elevation. There are a lot of arguments to produce different plots and figures. Some of the ones I find most useful are below. Note when years aren’t specified, all years are included by default.

plotPISpecies(location = "BASHAR", facet = T, main_groups = T, plotly = T)
plotPISpecies(park = "BOHA", facet = T, main_groups = T)

plotPISpecies(location = "SHIHAR", rev_axis = T, facet = T)

plotPISpecies(location = "OTTPOI", species = c("FUCSPP", "ASCNOD"), plotly = T)

PhotoPlot Cover

Plots the photoplot cover summarized as median cover and middle 50% distribution of cover across the photoplots within a target species. Note that there are a lot of arguments that produce different plots and figures (all explained in the help). Here are a few I tend to use the most.

plotPhotoCover(park = "ACAD", target_species = "Barnacle", plotly = T)
plotPhotoCover(location = "LITHUN", main_groups = T) 

plotPhotoCover(location = "LITHUN", top_spp = 3)

plotPhotoCover(location = "LITHUN", top_spp = 3, plotly = T, xlab = NULL, plot_title = "Little Hunter")
plotPhotoCover(location = "LITHUN", main_groups = T, target_species = "Fucus", plotly = T)
plotPhotoCover(location = "BASHAR", main_groups = T, heatmap = TRUE)

Motile Inverts

Plot the Counts

plotMotileInvertCounts(location = "OUTBRE", years = 2013:2021)

plotMotileInvertCounts(location = "OUTBRE", years = 2013:2021, plotly = T)

Plot the measurements

plotMotileInvertMeas(location = "SHIHAR", years = 2013:2019)

Echinoderms

Plot the Counts

plotEchinoCounts(location = "OUTBRE", years = 2013:2021)

plotEchinoCounts(location = "OUTBRE", years = 2013:2021, plotly = T)

Plot the measurements

plotEchinoMeas(location = "SHIHAR", years = 2013:2019)

Water temp 

plotWaterTemp(park = "ACAD", years = 2022, facet_col = 1)

plotWaterTemp(location = "BASHAR", years = 2011:2022)

Buoy Data 

plotBuoyData(park = "ACAD", metric = 'all')

## TableGrob (2 x 1) "arrange": 2 grobs
##   z
## 1 1
## 2 2
##       cells
## 1 (1-1,1-1)
## 2 (2-2,1-1)
##      name
## 1 arrange
## 2 arrange
##             grob
## 1 gtable[layout]
## 2 gtable[layout]
plotBuoyData(park = "ACAD", metric = "temp", year = 2022)

Rocky ggplot theme

The default ggplot aesthetics are too busy, and require several lines of code to turn off. For every package, I create a theme that turns those off and can just be run with the ggplot code. For this package use theme_rocky() as shown below.

dat <- sumPhotoCover(location = "SHIHAR", target_species = "Ascophyllum", species = "ASCNOD")

library(ggplot2)
ggplot(dat, aes(x = Year, y = median_cover)) +
  geom_point() +
  theme_rocky()